Concrete types, towards GPU support

.github/workflows/CompatHelper.yml

@@ -1,4 +1,5 @@
 name: CompatHelper
+
 on:
   schedule:
     - cron: 0 0 * * 0 # weekly
@@ -8,13 +9,25 @@ jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Pkg.add("CompatHelper")
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main()
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }} # need ssh
-        run: julia -e 'using CompatHelper; CompatHelper.main()'
-
-# based on:
-# https://github.com/JuliaRegistries/CompatHelper.jl
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/Documentation.yml

@@ -2,7 +2,11 @@ name: Documentation
 
 on:
   pull_request:
+    paths-ignore:
+      - 'README.md'
   push:
+    paths-ignore:
+      - 'README.md'
     branches:
       - 'main'
       - 'release-'
@@ -15,8 +19,8 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: '1.6'
-      - name: Cache artifacts
+          version: '1'
+      - name: CacheArtifacts
         uses: actions/cache@v1
         env:
           cache-name: cache-artifacts
@@ -27,13 +31,13 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - name: Install dependencies
+      - name: InstallDependencies
         run: |
           julia --project=docs/ -e '
-          ENV["JULIA_PKG_SERVER"] = ""
-          using Pkg
-          Pkg.develop(PackageSpec(path=pwd()))
-          Pkg.instantiate()'
+            ENV["JULIA_PKG_SERVER"] = ""
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
       - name: BuildAndDeploy
         env:
 # https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#Authentication:-GITHUB_TOKEN

.github/workflows/ci.yml

@@ -0,0 +1,42 @@
+name: CI
+
+on:
+  create:
+    tags:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - '**.md'
+      - 'docs/**'
+  pull_request:
+    paths-ignore:
+      - '**.md'
+      - 'docs/**'
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.version == 'nightly' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ['1.6', '1', 'nightly']
+        os: [ubuntu-latest, windows-latest, macOS-latest]
+    steps:
+      - uses: actions/checkout@v2
+#     - name: "Set up Julia"
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.version }}
+#     - name: "Unit Test"
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-runtest@latest
+#     - name: "Cover"
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        if: ${{ matrix.version == '1' && matrix.os == 'ubuntu-latest' }}
+        with:
+          file: lcov.info

.github/workflows/clean.yml

@@ -0,0 +1,28 @@
+# https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#gh-pages-Branch
+
+name: DocPreviewCleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.gitignore

@@ -16,6 +16,7 @@ deps/src/
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
+docs/src/generated/
 
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be

docs/Project.toml

@@ -1,19 +1,18 @@
 [deps]
+BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 ImagePhantoms = "71a99df6-f52c-4da1-bd2a-69d6f37f3252"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearMapsAA = "599c1a8e-b958-11e9-0d14-b1e6b2ecea07"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 MIRTjim = "170b2178-6dee-4cb0-8729-b3e8b57834cc"
+NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 SPECTrecon = "ab1be465-a7f0-4423-9048-0ee774b70ed9"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulRecipes = "42071c24-d89e-48dd-8a24-8a12d9b8861f"
-
-[compat]
-Distributions = "0.25"
-Documenter = "0.27.7"
-ImagePhantoms = "0.0.5"
-LinearMapsAA = "0.7"
-Literate = "2.9.3"
-MIRTjim = "0.13"
+Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
+ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"

docs/lit/examples/1-overview.jl

@@ -15,6 +15,7 @@ using LinearAlgebra: mul!
 using LinearMapsAA: LinearMapAA
 using Plots: scatter, plot!, default; default(markerstrokecolor=:auto)
 using Plots # @animate, gif
+using InteractiveUtils: versioninfo
 
 # The following line is helpful when running this example.jl file as a script;
 # this way it will prompt user to hit a key after each figure is displayed.
@@ -216,3 +217,15 @@ anim = @animate for i in 1:nview
     )
 end
 gif(anim, "views.gif", fps = 8)
+
+
+# ### Reproducibility
+
+# This page was generated with the following version of Julia:
+
+io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
+
+
+# And with the following package versions
+
+import Pkg; Pkg.status()

docs/lit/examples/3-psf.jl

@@ -64,7 +64,7 @@ jim(image, "Original image")
 
 px = 11
 nview = 1 # for simplicity in this illustration
-psf = repeat(psf_gauss( ; ny, px), 1, 1, 1, nview)
+psf = repeat(psf_gauss( ; ny=nx, px), 1, 1, 1, nview)
 jim(psf, "PSF for each of $nx planes")
 
 
@@ -111,7 +111,7 @@ jim(adj, "Adjoint of PSF modeling")
 using LinearMapsAA: LinearMapAA
 
 nx, nz, px = 10, 7, 5 # small size for illustration
-psf3 = psf_gauss( ; ny, px)
+psf3 = psf_gauss( ; ny=nx, px)
 plan = plan_psf( ; nx, nz, px, T)
 idim = (nx,nx,nz)
 odim = (nx,nx,nz)

docs/lit/examples/4-mlem.jl

@@ -100,7 +100,7 @@ function mlem(x0, ynoisy, background, A; niter::Int = 20)
     all(>(0), background) || throw("need background > 0")
     x = copy(x0)
     asum = A' * ones(eltype(ynoisy), size(ynoisy))
-	time0 = time()
+    time0 = time()
     for iter = 1:niter
         @show iter, extrema(x), time() - time0
         ybar = A * x .+ background # forward model
@@ -119,7 +119,7 @@ function mlem!(x, ynoisy, background, A; niter::Int = 20)
     ybar = similar(ynoisy)
     yratio = similar(ynoisy)
     back = similar(x)
-	time0 = time()
+    time0 = time()
     for iter = 1:niter
         @show iter, extrema(x), time() - time0
         mul!(ybar, A, x)